DOCSLIB.ORG

Mouse Sympk Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Sympk Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Sympk Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Sympk conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Sympk gene (NCBI Reference Sequence: NM_026605 ; Ensembl: ENSMUSG00000023118 ) is located on Mouse chromosome 7. 27 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 27 (Transcript: ENSMUST00000023882). Exon 4~5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Sympk gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-127O11 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous ofr a transgenic gene disruption exhibit anemia at E15 and hydrops fetalis. Exon 4 starts from about 4.45% of the coding region. The knockout of Exon 4~5 will result in frameshift of the gene. The size of intron 3 for 5'-loxP site insertion: 1362 bp, and the size of intron 5 for 3'-loxP site insertion: 3654 bp. The size of effective cKO region: ~710 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 2 3 4 5 27 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Sympk Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(7210bp) | A(22.41% 1616) | C(25.58% 1844) | T(29.21% 2106) | G(22.8% 1644) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN -------------------------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr7 + 19027294 19030293 3000 browser details YourSeq 144 1584 1889 3000 81.6% chr18 - 46356795 46356973 179 browser details YourSeq 85 2464 2638 3000 92.2% chr7 + 98188041 98188220 180 browser details YourSeq 83 2449 2599 3000 87.7% chr10 + 115345595 115345777 183 browser details YourSeq 73 2464 2606 3000 80.2% chr6 + 139634694 139634844 151 browser details YourSeq 70 2466 2586 3000 82.8% chr10 - 39081149 39081279 131 browser details YourSeq 69 2514 2629 3000 90.9% chr18 - 60555691 60555815 125 browser details YourSeq 67 2466 2617 3000 90.3% chr11 - 77292552 77292712 161 browser details YourSeq 67 2486 2634 3000 92.5% chr4 + 121134920 121135088 169 browser details YourSeq 67 2518 2605 3000 94.6% chr14 + 105998992 105999087 96 browser details YourSeq 64 2464 2581 3000 79.1% chr3 + 40956107 40956228 122 browser details YourSeq 63 2514 2603 3000 89.8% chr2 + 74910446 74910543 98 browser details YourSeq 63 2537 2636 3000 92.0% chr1 + 133079271 133079377 107 browser details YourSeq 62 2524 2620 3000 91.8% chr12 + 3601543 3601648 106 browser details YourSeq 61 2486 2619 3000 93.1% chr11 - 94584081 94584392 312 browser details YourSeq 61 2463 2565 3000 88.0% chr11 - 50824845 50824946 102 browser details YourSeq 61 2439 2582 3000 93.0% chr19 + 59028647 59028806 160 browser details YourSeq 61 2516 2606 3000 92.9% chr14 + 40865707 40865805 99 browser details YourSeq 59 2460 2622 3000 92.9% chr6 - 113223214 113223387 174 browser details YourSeq 59 2466 2586 3000 94.1% chr6 - 12199205 12199326 122 Note: The 3000 bp section upstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN -------------------------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr7 + 19031004 19034003 3000 browser details YourSeq 384 1216 1722 3000 91.8% chr7 - 15836594 15837109 516 browser details YourSeq 371 1228 1722 3000 90.0% chr9 + 40768429 40769122 694 browser details YourSeq 355 1232 1716 3000 90.5% chr2 - 84029362 84030141 780 browser details YourSeq 345 1249 1722 3000 92.9% chr19 + 16711193 16711666 474 browser details YourSeq 331 1277 1722 3000 91.3% chr6 - 113205582 113206366 785 browser details YourSeq 329 1277 1721 3000 90.5% chr2 - 146277297 146278086 790 browser details YourSeq 315 1251 1722 3000 90.1% chr19 - 52875102 52875790 689 browser details YourSeq 280 1350 1721 3000 91.2% chr14 + 94516611 94517398 788 browser details YourSeq 274 1342 1722 3000 93.2% chr18 - 46545306 46546091 786 browser details YourSeq 273 1399 1784 3000 90.5% chr13 - 42551001 42551760 760 browser details YourSeq 271 1216 1722 3000 87.3% chr19 + 11704181 11704553 373 browser details YourSeq 269 1388 1767 3000 90.0% chr9 - 84239187 84239780 594 browser details YourSeq 269 1389 1722 3000 91.7% chr12 - 101653579 101653915 337 browser details YourSeq 269 1399 1722 3000 93.8% chr11 - 26165623 26165948 326 browser details YourSeq 269 1243 1722 3000 92.0% chr9 + 16519094 16519662 569 browser details YourSeq 267 1402 2181 3000 85.3% chr2 - 105876220 105876561 342 browser details YourSeq 267 1399 1713 3000 93.5% chr1 + 98010068 98010388 321 browser details YourSeq 264 1388 1716 3000 91.4% chr19 + 41252910 41253237 328 browser details YourSeq 263 1399 1722 3000 92.9% chr8 + 10469245 10469570 326 Note: The 3000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 4 of 8 https://www.alphaknockout.com Gene and protein information: Sympk symplekin [ Mus musculus (house mouse) ] Gene ID: 68188, updated on 12-Aug-2019 Gene summary Official Symbol Sympk provided by MGI Official Full Name symplekin provided by MGI Primary source MGI:MGI:1915438 See related Ensembl:ENSMUSG00000023118 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as SPK; SYM; AA125406; AI449890; 1500016F02Rik; 4632415H16Rik Expression Ubiquitous expression in testis adult (RPKM 36.3), ovary adult (RPKM 34.7) and 28 other tissues See more Orthologs human all Genomic context Location: 7; 7 A3 See Sympk in Genome Data Viewer Exon count: 29 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (19024377..19054623) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (19609726..19639971) Chromosome 7 - NC_000073.6 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 8 transcripts Gene: Sympk ENSMUSG00000023118 Description symplekin [Source:MGI Symbol;Acc:MGI:1915438] Gene Synonyms 1500016F02Rik, 4632415H16Rik Location Chromosome 7: 19,024,377-19,054,618 forward strand. GRCm38:CM001000.2 About this gene This gene has 8 transcripts (splice variants), 188 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Sympk- ENSMUST00000023882.13 4116 1288aa ENSMUSP00000023882.7 Protein coding CCDS52051 F8WJD4 TSL:1 201 GENCODE basic APPRIS P1 Sympk- ENSMUST00000153976.7 827 198aa ENSMUSP00000121540.1 Protein coding - D3Z2M2 CDS 3' 208 incomplete TSL:5 Sympk- ENSMUST00000130328.1 469 143aa ENSMUSP00000115900.1 Protein coding - F6UJ99 CDS 5' 202 incomplete TSL:3 Sympk- ENSMUST00000146903.7 4781 234aa ENSMUSP00000138740.1 Nonsense mediated - S4R2Q3 TSL:1 206 decay Sympk- ENSMUST00000137287.2 4760 No - Retained intron - - TSL:1 204 protein Sympk- ENSMUST00000131230.1 636 No - Retained intron - - TSL:2 203 protein Sympk- ENSMUST00000148861.7 1099 No - lncRNA - - TSL:1 207 protein Sympk- ENSMUST00000138440.1 799 No - lncRNA - - TSL:3 205 protein Page 6 of 8 https://www.alphaknockout.com 50.24 kb Forward strand 19.02Mb 19.03Mb 19.04Mb 19.05Mb 19.06Mb Genes (Comprehensive set... Sympk-201 >protein coding Rsph6a-201 >protein coding Sympk-208 >protein coding Sympk-205 >lncRNA Sympk-207 >lncRNA Sympk-204 >retained intron Sympk-202 >protein coding Sympk-206 >nonsense mediated decay Sympk-203 >retained intron Rsph6a-202 >protein coding Rsph6a-203 >lncRNA Contigs < AC170864.2 Genes < Foxa3-201protein coding (Comprehensive set... Regulatory Build 19.02Mb 19.03Mb 19.04Mb 19.05Mb 19.06Mb Reverse strand 50.24 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding RNA gene processed transcript Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000023882 30.24 kb Forward strand Sympk-201 >protein coding ENSMUSP00000023... MobiDB lite Low complexity (Seg) Superfamily Armadillo-type fold Pfam Symplekin/Pta1, N-terminal Symplekin C-terminal PANTHER PTHR15245 Symplekin/Pta1 Gene3D Armadillo-like helical All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend frameshift variant inframe deletion missense variant splice region variant synonymous variant Scale bar 0 200 400 600 800 1000 1288 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
Load more

Recommended publications
  • Nuclear and Mitochondrial Genome Defects in Autisms
    UC Irvine UC Irvine Previously Published Works Title Nuclear and mitochondrial genome defects in autisms. Permalink https://escholarship.org/uc/item/8vq3278q Journal Annals of the New York Academy of Sciences, 1151(1) ISSN 0077-8923 Authors Smith, Moyra Spence, M Anne Flodman, Pamela Publication Date 2009 DOI 10.1111/j.1749-6632.2008.03571.x License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California THE YEAR IN HUMAN AND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome Defects in Autisms Moyra Smith, M. Anne Spence, and Pamela Flodman Department of Pediatrics, University of California, Irvine, California In this review we will evaluate evidence that altered gene dosage and structure im- pacts neurodevelopment and neural connectivity through deleterious effects on synap- tic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrixtm SNP 6.0 microar- ray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Col- lectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chro- mosome.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • HSF1 Polyclonal Antibody Catalog # AP70419
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 HSF1 Polyclonal Antibody Catalog # AP70419 Specification HSF1 Polyclonal Antibody - Product Information Application WB Primary Accession Q00613 Reactivity Human, Mouse Host Rabbit Clonality Polyclonal HSF1 Polyclonal Antibody - Additional Information Gene ID 3297 Other Names HSF1; HSTF1; Heat shock factor protein 1; HSF 1; Heat shock transcription factor 1; HSTF 1 Dilution WB~~Western Blot: 1/500 - 1/2000. Immunohistochemistry: 1/100 - 1/300. HSF1 Polyclonal Antibody - Background Immunofluorescence: 1/200 - 1/1000. ELISA: 1/10000. Not yet tested in other Function as a stress-inducible and applications. DNA-binding transcription factor that plays a central role in the transcriptional activation of Format the heat shock response (HSR), leading to the Liquid in PBS containing 50% glycerol, 0.5% expression of a large class of molecular BSA and 0.02% sodium azide. chaperones heat shock proteins (HSPs) that protect cells from cellular insults' damage Storage Conditions -20℃ (PubMed:1871105, PubMed:11447121, PubMed:1986252, PubMed:7760831, PubMed:7623826, PubMed:8946918, PubMed:8940068, PubMed:9341107, HSF1 Polyclonal Antibody - Protein Information PubMed:9121459, PubMed:9727490, PubMed:9499401, PubMed:9535852, Name HSF1 (HGNC:5224) PubMed:12659875, PubMed:12917326, PubMed:15016915, PubMed:25963659, Synonyms HSTF1 PubMed:26754925). In unstressed cells, is present in a HSP90-containing multichaperone Function complex that maintains it in a non-DNA-binding Functions
    [Show full text]
  • Symplekin and Transforming Acidic Coiled-Coil Containing Protein 3 Support the Cancer Cell Mitotic Spindle
    SYMPLEKIN AND TRANSFORMING ACIDIC COILED-COIL CONTAINING PROTEIN 3 SUPPORT THE CANCER CELL MITOTIC SPINDLE Kathryn M. Cappell A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctorate of Philosophy in the Department of Pharmacology, School of Medicine. Chapel Hill 2011 Approved by: Advisor: Dr. Angelique Whitehurst Reader: Dr. David Siderovski Reader: Dr. Channing Der Reader: Dr. Pilar Blancafort Reader: Dr. Mohanish Deshmukh ABSTRACT KATHRYN CAPPELL: Symplekin and Transforming Acidic Coiled-Coil Containing Protein 3 Support the Cancer Cell Mitotic Spindle (Under the direction of Dr. Angelique Whitehurst) An increased rate of proliferation in cancer cells, combined with abnormalities in spindle architecture, places tumors under increased mitotic stress. Previously, our laboratory performed a genome-wide paclitaxel chemosensitizer screen to identify genes whose depletion sensitizes non- small cell lung cancer (NSCLC) cells to mitotic stress induced by paclitaxel treatment. This screen uncovered a cohort of genes that are required for viability only in the presence of paclitaxel. Two genes uncovered in this screen were the polyadenylation scaffold symplekin and the gametogenic protein transforming acidic coiled-coil containing protein 3 (TACC3). Herein, we examine the impact of polyadenylation and gametogenesis on the tumor cell mitotic spindle. First, we demonstrate that depletion of SYMPK and other polyadenylation components sensitizes many NSCLC cells, but not normal immortalized lines, to paclitaxel by inducing mitotic errors and leading to abnormal mitotic progression. Second, we demonstrate that multiple gametogenic genes are required for normal microtubule dynamics and mitotic spindle formation in the presence of paclitaxel.
    [Show full text]
  • Phospho-HSF1 (Ser326) Rabbit Pab 产品说明书
    正能生物 Phospho-HSF1 (Ser326) Rabbit pAb 货号：384621 Size 100ul 50ul Antibody type Primary antibody Conjugation Unconjugated Modification Phosphoralated Isotype Rabbit IgG Host Rabbit Application WB , IHC-P , IHC-F , ICC/IF , FC , IP Purification Affinity purified Cross reactivity Human Gene name HSF1 Alternative names HSTF1 Gene symbol HSTF1 Description Swiss-Prot Acc.Q00613.Function as a stress-inducible and DNA-binding transcription factor that plays a central role in the transcriptional activation of the heat shock response (HSR), leading to the expression of a large class of molecular chaperones heat shock proteins (HSPs) that protect cells from cellular insults' damage (PubMed:1871105, PubMed:11447121, PubMed:1986252, PubMed:7760831, PubMed:7623826, PubMed:8946918, PubMed:8940068, PubMed:9341107, PubMed:9121459, PubMed:9727490, PubMed:9499401, PubMed:9535852, PubMed:12659875, PubMed:12917326, PubMed:15016915, PubMed:25963659, PubMed:26754925). In unstressed cells, is present in a HSP90-containing multichaperone complex that maintains it in a non-DNA-binding inactivated monomeric form (PubMed:9727490, PubMed:11583998, PubMed:16278218). Upon exposure to heat and other stress stimuli, undergoes homotrimerization and activates HSP gene transcription through binding to site-specific heat shock elements (HSEs) present in the promoter regions of HSP genes (PubMed:1871105, PubMed:1986252, PubMed:8455624, PubMed:7935471, PubMed:7623826, PubMed:8940068, PubMed:9727490, PubMed:9499401, PubMed:10359787, PubMed:11583998, PubMed:12659875, PubMed:16278218, PubMed:25963659, PubMed:26754925). Activation is reversible, and during the attenuation and recovery phase period of the HSR, returns to its unactivated form (PubMed:11583998, PubMed:16278218). Binds to inverted 5'-NGAAN-3' pentamer DNA sequences (PubMed:1986252, PubMed:26727489). Binds to chromatin at heat shock gene promoters (PubMed:25963659).
    [Show full text]
  • Quantitative SUMO Proteomics Reveals the Modulation of Several
    www.nature.com/scientificreports OPEN Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated Received: 10 October 2017 Accepted: 28 March 2018 proteins and an anti-senescence Published: xx xx xxxx function of UBC9 Francis P. McManus1, Véronique Bourdeau2, Mariana Acevedo2, Stéphane Lopes-Paciencia2, Lian Mignacca2, Frédéric Lamoliatte1,3, John W. Rojas Pino2, Gerardo Ferbeyre2 & Pierre Thibault1,3 Several regulators of SUMOylation have been previously linked to senescence but most targets of this modifcation in senescent cells remain unidentifed. Using a two-step purifcation of a modifed SUMO3, we profled the SUMO proteome of senescent cells in a site-specifc manner. We identifed 25 SUMO sites on 23 proteins that were signifcantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation. Many cellular mechanisms of defense have evolved to reduce the onset of tumors and potential cancer develop- ment. One such mechanism is cellular senescence where cells undergo cell cycle arrest in response to various stressors1,2. Multiple triggers for the onset of senescence have been documented. While replicative senescence is primarily caused in response to telomere shortening3,4, senescence can also be triggered early by a number of exogenous factors including DNA damage, elevated levels of reactive oxygen species (ROS), high cytokine signa- ling, and constitutively-active oncogenes (such as H-RAS-G12V)5,6.
    [Show full text]
  • Related Regulators of 3′ UTR Processing with KAPAC Andreas J
    Gruber et al. Genome Biology (2018) 19:44 https://doi.org/10.1186/s13059-018-1415-3 METHOD Open Access Discovery of physiological and cancer- related regulators of 3′ UTR processing with KAPAC Andreas J. Gruber† , Ralf Schmidt†, Souvik Ghosh, Georges Martin, Andreas R. Gruber, Erik van Nimwegen and Mihaela Zavolan* Abstract 3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma. Keywords: Cleavage and polyadenylation, APA, CFIm, KAPAC, PAQR, HNRNPC, PTBP1, Prostate adenocarcinoma, Glioblastoma, Colon adenocarcinoma Background signal, consisting of the CPSF1, CPSF4, FIP1L1, and The 3′ ends of most eukaryotic mRNAs are generated WDR33 proteins, has been identified [6, 7]. through endonucleolytic cleavage and polyadenylation Most genes have multiple poly(A) sites (PAS), which (CPA) [1–3]. These steps are carried out in mammalian are differentially processed across cell types [8], likely cells by a 3′ end processing complex composed of the due to cell type-specific interactions with RNA-binding cleavage and polyadenylation specificity factor (which in- proteins (RBPs). The length of 3′ UTRs is most strongly cludes the proteins CPSF1 (also known as CPSF160), dependent on the mammalian cleavage factor I (CFIm), CPSF2 (CPSF100), CPSF3 (CPSF73), CPSF4 (CPSF30), which promotes the use of distal poly(A) sites [5, 9–12].
    [Show full text]
  • Antisense Oligonucleotide-Based Therapeutic Against Menin for Triple-Negative Breast Cancer Treatment
    biomedicines Article Antisense Oligonucleotide-Based Therapeutic against Menin for Triple-Negative Breast Cancer Treatment Dang Tan Nguyen 1,†, Thi Khanh Le 1,2,† , Clément Paris 1,†, Chaïma Cherif 1 , Stéphane Audebert 3 , Sandra Oluchi Udu-Ituma 1,Sébastien Benizri 4 , Philippe Barthélémy 4 , François Bertucci 1, David Taïeb 1,5 and Palma Rocchi 1,* 1 Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, 13273 Marseille, France; [email protected] (D.T.N.); [email protected] (T.K.L.); [email protected] (C.P.); [email protected] (C.C.); [email protected] (S.O.U.-I.); [email protected] (F.B.); [email protected] (D.T.) 2 Department of Life Science, University of Science and Technology of Hanoi (USTH), Hanoi 000084, Vietnam 3 Marseille Protéomique, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France; [email protected] 4 ARNA Laboratory, INSERM U1212, CNRS UMR 5320, University of Bordeaux, 33076 Bordeaux, France; [email protected] (S.B.); [email protected] (P.B.) 5 Biophysics and Nuclear Medicine Department, La Timone University Hospital, European Center for Research in Medical Imaging, Aix-Marseille University, 13005 Marseille, France * Correspondence: [email protected]; Tel.: +33-626-941-287 † These authors contributed equally. Citation: Nguyen, D.T.; Le, T.K.; Paris, C.; Cherif, C.; Audebert, S.; Abstract: The tumor suppressor menin has dual functions, acting either as a tumor suppressor or Oluchi Udu-Ituma, S.; Benizri, S.; as an oncogene/oncoprotein, depending on the oncological context.
    [Show full text]
  • NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer
    Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-7-2018 Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer Jairo Ramos [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Clinical Epidemiology Commons Recommended Citation Ramos, Jairo, "Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer" (2018). FIU Electronic Theses and Dissertations. 3872. https://digitalcommons.fiu.edu/etd/3872 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida DECIPHER MECHANISMS BY WHICH NUCLEAR RESPIRATORY FACTOR ONE (NRF1) COORDINATES CHANGES IN THE TRANSCRIPTIONAL AND CHROMATIN LANDSCAPE AFFECTING DEVELOPMENT AND PROGRESSION OF INVASIVE BREAST CANCER A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Jairo Ramos 2018 To: Dean Tomás R. Guilarte Robert Stempel College of Public Health and Social Work This dissertation, Written by Jairo Ramos, and entitled Decipher Mechanisms by Which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer, having been approved in respect to style and intellectual content, is referred to you for judgment.
    [Show full text]
  • A Strategy to Identify Housekeeping Genes Suitable for Analysis in Breast Cancer Diseases Tatiana M
    Tilli et al. BMC Genomics (2016) 17:639 DOI 10.1186/s12864-016-2946-1 RESEARCH ARTICLE Open Access A strategy to identify housekeeping genes suitable for analysis in breast cancer diseases Tatiana M. Tilli1, Cláudio da Silva Castro2, Jack A. Tuszynski3,4 and Nicolas Carels1* Abstract Background: The selection of suitable internal control genes is crucial for proper interpretation of real-time PCR data. Here we outline a strategy to identify housekeeping genes that could serve as suitable internal control for comparative analyses of gene expression data in breast cancer cell lines and tissues obtained by high throughput sequencing and quantitative real-time PCR (qRT-PCR). Methods: The strategy proposed includes the large-scale screening of potential candidate reference genes from RNA-seq data as well as their validation by qRT-PCR, and careful examination of reference data from the International Cancer Genome Consortium, The Cancer Genome Atlas and Gene Expression Omnibus repositories. Results: The identified set of reference genes, also called novel housekeeping genes that includes CCSER2, SYMPK, ANKRD17 and PUM1, proved to be less variable and thus potentially more accurate for research and clinical analyses of breast cell lines and tissue samples compared to the traditional housekeeping genes used to this end. Discussion: These results highlight the importance of a massive evaluation of housekeeping genes for their relevance as internal control for optimized intra- and inter-assay comparison of gene expression. Conclusion: We developed a strategy to identify and evaluate the significance of housekeeping genes as internal control for the intra- and inter-assay comparison of gene expression in breast cancer that could be applied to other tumor types and diseases.
    [Show full text]
  • The RET Receptor Is Linked to Stress Response Pathways
    [CANCER RESEARCH 64, 4453–4463, July 1, 2004] The RET Receptor Is Linked to Stress Response Pathways Shirley M. Myers and Lois M. Mulligan Division of Cancer Biology and Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada ABSTRACT viewed in Ref. 13). Furthermore, rearrangements of RET, resulting in juxtaposition of the RET kinase domain with a dimerization domain RET is a transmembrane receptor required for the development of from any of several other proteins, occur somatically in papillary neuroendocrine and urogenital cell types. Activation of RET has roles in cell growth, migration, or differentiation, yet little is known about the gene thyroid carcinoma (14). In each case, these mutations result in acti- expression patterns through which these processes are mediated. We have vation of the RET receptor, leading to inappropriate and/or increased generated cell lines stably expressing either the RET9 or RET51 protein RET-mediated signal transduction and resultant cell proliferation and isoforms and have used these to investigate RET-mediated gene expres- tumorigenesis. sion patterns by cDNA microarray analyses. As seen for many oncogenes, Activation of RET, either by ligand or through specific mutations, we identified altered expression of genes associated generally with cell– results in phosphorylation of multiple tyrosine residues that, in turn, cell or cell-substrate interactions and up-regulation of tumor-specific interact with specific adaptor molecules to trigger downstream sig- transcripts. We also saw increased expression of transcripts normally naling. Four of the tyrosines phosphorylated on RET activation, associated with neural crest or other RET-expressing cell types, suggesting these genes may lie downstream of RET activation in development.
    [Show full text]
  • Genome-Wide Analysis of Luhya and Maasai Genomes Reveals Signatures of Selection for Fertility, Prostate Cancer, Prostatitis and Vein Disease
    Journal of Cancer Prevention & Current Research Research Article Open Access Genome-wide analysis of luhya and maasai genomes reveals signatures of selection for fertility, prostate cancer, prostatitis and vein disease Abstract Volume 9 Issue 2 - 2018 Background & Aim: Selection pressure has left traceable molecular selection signatures within the human genomes. Identification of selection signatures is vital for Kiplangat Ngeno understanding the evolutionary processes shaping human adaptation and diversity in Animal Breeding and Genomics Group, Department of Animal disease susceptibility. In this study, genomes of Luhya and Maasai ethnic groups were Sciences, Egerton University, Kenya compared to identify selection signatures that may explain their genetic divergence. Correspondence: Kiplangat Ngeno, Department of Animal Materials and Methods: The population studied composed of 90 Luhyas’ and 31 Sciences, Egerton University, P.O. Box 536, 20115 Egerton, Maasais’ from Webuye and Kinyawa, Kenya respectively. Data were sourced from Kenya, Email [email protected] 1000 genomes project phase 3. These data were processed through similar statistical quality control protocols. Received: February 20, 2017 | Published: April 02, 2018 Results: Datasets were processed individually then merged; resulting in 1,480,668 high-quality SNPs. Genomic scan using F-statistics (Fst) method revealed putative genomic selection signatures. Fifty-five genomic regions (high Fst, 5.6 to 9.8). These regions overlapped with 21 genes. Three genes (C9orf24, BAZ2A, and SYMPK) out of the 21 are associated with the missense variants that could explain partially the genetic divergence and variation in fertility and disease susceptibility between these populations. The genes are associated with spermatogenesis (C9orf24 gene), prostate cancer and prostatitis (BAZ2A gene) and vein disease (SYMPK gene).
    [Show full text]